 From 1988 to 1994, Marburger chaired Universities Research Association, the organization that operated Fermilab and oversaw construction of the ill-fated Superconducting Super Collider, an experience that is credited with convincing him of the influence government had in how science is carried out.During this time he also served as a trustee of Princeton University.He stepped down as President of Stony Brook University in 1994, and began doing research again as a member of the faculty.